Backup systems and methods are disclosed for a virtual computing environment. Certain examples include a system having a backup management server that communicates with a host server having at least one virtual machine. The management server coordinates with the host server to perform backup copies of entire virtual machine disks from outside the guest operating system of the virtual machine. In certain examples, such backup systems further utilize a volume shadow copy service executing on the host server to quiesce virtual machine applications to put data in a consistent state to be backed up. The backup system then utilizes hypervisor snapshot capabilities of the host server to record intended changes to the virtual machine disk files while such files are being copied (e.g., backed up) by the host server. Such recorded changes can be later committed to the virtual machine disk files once the backup operation has completed.